Research workbench
Crystal structure of streptococcus suis dpr with cobalt
Analyse Crystal structure of streptococcus suis dpr with cobalt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XJM
- Type
- protein
- Length
- 1,811 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- P0CB53
- Ligands
- CO, CA, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | DNA protection during starvation protein (EC 1.16.-.-) | protein | 150 | 76% helix, 0% strand | P0CB53 |
| B, D, K | DNA protection during starvation protein (EC 1.16.-.-) | protein | 152 | 74% helix, 0% strand | P0CB53 |
| F, H, I, J, L | DNA protection during starvation protein (EC 1.16.-.-) | protein | 151 | 75% helix, 0% strand | P0CB53 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 12 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
- CA · Calcium ion · metal · 8 copies · chains B, C, L, E, F, J, H, K, I
- CL · Chloride ion · ion · 3 copies · chains A, I, J
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains C, E, L, D, G, I, B, F, J, A, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.74 | 0.94 | 26 | empty |
| 2 | 193 | 0.70 | 0.88 | 28 | empty |
| 3 | 236 | 0.69 | 0.85 | 33 | empty |
| 4 | 212 | 0.68 | 0.86 | 29 | empty |
| 5 | 204 | 0.67 | 0.85 | 27 | empty |
Interfaces
30 interfaces between chains.
- E–G · 1200 Ų buried · 17 hydrogen bonds · protein-protein
- I–K · 1196 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1190 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1186 Ų buried · 18 hydrogen bonds · protein-protein
- J–L · 1186 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2XJM · Crystal structure of Streptococcus suis Dpr with cobalt · the same entry in another collection · chain F against F, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0CB53
- Elsewhere: RCSB PDB 2XJM · PDBe 2XJM · UniProt P0CB53
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